JohnLonginotto

import random
import argparse

parser = argparse.ArgumentParser(     description="https://www.youtube.com/watch?v=7S94ohyErSw&t=90")
parser.add_argument("-t",   "--tests",             default=50,     type=int, help='The number of tests to average')
parser.add_argument("-tp",  "--true_positives",    required=True,  type=int, help='The actual number of True Positives')
parser.add_argument("-tn",  "--true_negatives",    required=True,  type=int, help='The actual number of True Negatives (Total things - True Positives)')
parser.add_argument("-tpa", "--true_positives_A",  required=True,  type=int, help='True Positives tool A detects')
parser.add_argument("-fpa", "--false_positives_A", required=True,  type=int, help='False Positives tool A detects')
parser.add_argument("-tpb", "--true_positives_B",  required=True,  type=int, help='True Positives tool B detects')

JohnLonginotto

if [ "`tail -c 28 /path/to/your.bam`" != "`echo -n -e '\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00\x42\x43\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00'`" ]; then echo 'File Truncated'; else echo 'File Good!';  fi

JohnLonginotto

#!/usr/bin/env python3
import os
import csv
import argparse

parser = argparse.ArgumentParser(description='Process output from Mash')
parser.add_argument('-i', '--input',    help='input file',     metavar='FILE',   required=True)
parser.add_argument('-o', '--output',   help='output file',    metavar='FILE'                 )
parser.add_argument('-a', '--alias',    help='alias file',     metavar='FILE'                 )
parser.add_argument('-n', '--nearness', help='invert distance',action="store_true"            )

JohnLonginotto

class stat:
    def __init__(self,INFO):
        self.DESCRIPTION =  ['Demo for harmbrugge', 'ENSMUSG00000051951'] 
        self.LINKABLE = True 
        self.SQL = 'TEXT'
        self.dependencies = ['CHR','POS','SEQ']
        self.before = '''
import intervaltree
GTF_chromosomes = {}
with open('/Users/John/Downloads/Mus_musculus.GRCm38.86.gtf','rb') as f:

JohnLonginotto

import sys
reads = sys.argv[1]
index = sys.argv[2]
all_readIDs = set()

# Re-written the code below to only ever read the first row:
with open(reads, "r") as read_file:
	while True:
		try:
			line1 = next(read_file)

JohnLonginotto

import sys
reads = sys.argv[1]
index = sys.argv[2]

# Get all read ids:
all_readIDs = set() 	# Using a set because it will be quicker to find things in later. 
			# A list would require python to check every item in the list. 
			# A set can be thought of as an always-sorted list (elements are added in their sorted order) with no duplication of elements.
			# The sorted order is based on the hash() value of the items however, which is essentially a random number.

JohnLonginotto

# Stuff you might have to change depending on your package manager the IP of your client:
# (these settings will work well for EC2 though)
Listen 10.8.0.1
User tinyproxy
Group tinyproxy

# More is better/faster:
MinSpareServers 10
MaxSpareServers 50
StartServers 25

JohnLonginotto

# Non-Windows only:
user nobody
group nogroup

# Common for everything else:
client
dev tun
proto tcp-client
remote 54.152.94.74 443
resolv-retry infinite

JohnLonginotto

# STUFF YOU COULD CHANGE TO REFLECT YOUR SYSTEM BETTER:
export KEY_COUNTRY="UK"
export KEY_PROVINCE="London"
export KEY_CITY="London"
export KEY_ORG="MyVPN"
export KEY_EMAIL="my@email.com"
export KEY_OU="MyVPN"

# STUFF YOU SHOULDNT CHANGE
export EASY_RSA="/etc/openvpn/easy-rsa"

JohnLonginotto

management localhost 6666     # Allows you to telnet into localhost 6666 to see the status. Although openvpn has logs, you can find out a lot more (like who is currently using on the VPN) through the management service
port 443                      # By using port 443 for all of our VPN communications, our network traffic will look very similar to standard HTTPS traffic.
client-to-client              # Allows two clients of the VPN to talk to one another (home computer to work computer for example)
keepalive 10 120              # Defaults
mssfix                        # Kept due to Cargo Cult reasons...
proto tcp                     # udp is faster, but so much less reliable its not worth it. Use TCP.
dev tun                       # We're making a tunnel so we want to make the tun kind of VPN.
ca ca.crt                     # we'll make this next
cert server.crt               # we'll make this next
key server.key                # we'll make this next